Table 6

Excess Span and Largest Homogeneous Cluster Size for SCOP C Class folds.

Excess Span Size§

Largest Homog. Cluster (%) +


Row

fold

SCOP fold description

Ndom*

Nfam#

VAST

SHEBA

DALI

INT◊

VAST

SHEBA

DALI

Nc$


CONSISTENT FOLDS

1

c.100

Thiamin pyrophosphokinase, catalytic domain

2

1

0

0

0

0

100

100

100

1

2

c.101

Undecaprenyl diphosphate synthase

2

1

0

0

0

0

100

100

100

1

3

c.106

SurE-like

2

1

0

0

0

0

100

100

100

1

4

c.109

PEP carboxykinase N-terminal domain

4

1

0

0

0

0

100

100

100

1

5

c.114

YchN-like

2

1

0

0

0

0

100

100

100

1

6

c.117

Amidase signature (AS) enzymes

3

1

0

0

0

0

100

100

100

1

7

c.16

Lumazine synthase

3

1

0

0

0

0

100

100

100

1

8

c.17

Caspase-like

3

2

0

0

0

0

100

100

100

1

9

c.22

Ribosomal protein L4

2

1

0

0

0

0

100

100

100

1

10

c.27

Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain

3

1

0

0

0

0

100

100

100

1

11

c.28

Cryptochrome/photolyase, N-terminal domain

4

1

0

0

0

0

100

100

100

1

12

c.32

Tubulin, GTPase domain

2

1

0

0

0

0

100

100

100

1

13

c.33

Cysteine hydrolase

3

2

0

0

0

0

100

100

100

1

14

c.34

DFP DNA/pantothenate metabolism flavoprotein

2

1

0

0

0

0

100

100

100

1

15

c.36

Thiamin diphosphate-binding fold (THDP-binding)

19

4

0

0

0

0

100

100

100

1

16

c.39

Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT)

2

1

0

0

0

0

100

100

100

1

17

c.42

Arginase/deacetylase

3

2

0

0

0

0

100

100

100

1

18

c.43

CoA-dependent acyltransferases

7

3

0

0

0

0

100

100

100

1

19

c.5

MurCD N-terminal domain

2

1

0

0

0

0

100

100

100

1

20

c.50

Leucine aminopeptidase (Aminopeptidase A), N-terminal domain

2

1

0

0

0

0

100

100

100

1

21

c.59

MurD-like peptide ligases, peptide-binding domain

5

2

0

0

0

0

100

100

100

1

22

c.6

Cellulases

3

1

0

0

0

0

100

100

100

1

23

c.62

vWA-like

8

2

0

0

0

0

100

100

100

1

24

c.65

Formyltransferase

3

1

0

0

0

0

100

100

100

1

25

c.67

PLP-dependent transferases

35

6

0

0

0

0

100

100

100

1

26

c.68

Nucleotide-diphospho-sugar transferases

15

12

0

0

0

0

100

100

100

1

27

c.7

PFL-like glycyl radical enzymes

4

4

0

0

0

0

100

100

100

1

28

c.70

Nucleoside hydrolase

2

1

0

0

0

0

100

100

100

1

29

c.71

Dihydrofolate reductases

8

1

0

0

0

0

100

100

100

1

30

c.73

Carbamate kinase-like

2

2

0

0

0

0

100

100

100

1

31

c.74

AraD-like aldolase/epimerase

3

1

0

0

0

0

100

100

100

1

32

c.76

Alkaline phosphatase-like

6

3

0

0

0

0

100

100

100

1

33

c.77

Isocitrate/Isopropylmalate dehydrogenases

4

2

0

0

0

0

100

100

100

1

34

c.79

Tryptophan synthase beta subunit-like PLP-dependent enzymes

6

1

0

0

0

0

100

100

100

1

35

c.81

Formate dehydrogenase/DMSO reductase, domains 1–3

5

1

0

0

0

0

100

100

100

1

36

c.83

Aconitase iron-sulfur domain

2

1

0

0

0

0

100

100

100

1

37

c.86

Phosphoglycerate kinase

2

1

0

0

0

0

100

100

100

1

38

c.89

Phosphofructokinase

2

1

0

0

0

0

100

100

100

1


MODERATELY CONSISTENT FOLDS

39

c.25

Ferredoxin reductase-like, C-terminal NADP-linked domain

12

5

643

0

0

0

92

100

100

1

40

c.61

PRTase-like

17

2

0

0

68

0

100

100

88

1

41

c.82

ALDH-like

7

2

0

954

0

0

100

86

100

1

42

c.87

UDP-Glycosyltransferase/glycogen phosphorylase

6

6

0

937

0

0

100

83

100

1

43

c.116

alpha/beta knot

5

3

3

0

0

0

80

100

100

1

44

c.41

Subtilisin-like

4

2

0

0

1056

0

100

100

75

1

45

c.98

MurF and HprK N-domain-like

4

2

8

0

0

0

75

100

100

1

46

c.46

Rhodanese/Cell cycle control phosphatase

7

3

130

54

0

0

86

86

100

1

47

c.57

Molybdenum cofactor biosynthesis proteins

3

2

1056

0

0

0

67

100

100

1

48

c.93

Periplasmic binding protein-like I

13

1

3

0

0

0

62

100

100

1

49

c.45

(Phosphotyrosine protein) phosphatases II

12

2

0

0

267

0

100

100

58

1

50

c.107

DHH phosphoesterases

2

2

0

0

1058

0

100

100

50

1

51

c.18

DNA glycosylase

2

2

1057

0

0

0

50

100

100

1

52

c.108

HAD-like

11

10

1048

932

0

0

55

91

100

1

53

c.10

Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)

18

10

304

0

0

0

44

100

100

1

54

c.48

TK C-terminal domain-like

5

3

50

0

47

0

60

100

80

1

55

c.14

ClpP/crotonase

11

3

240

335

0

0

73

64

100

1

56

c.24

Methylglyoxal synthase-like

3

3

450

0

27

0

67

100

67

1

57

c.8

The "swivelling" beta/beta/alpha domain

10

8

0

28

4

0

100

80

40

1

58

c.63

CoA transferase

5

2

0

1

1

0

100

60

60

1

59

c.55

Ribonuclease H-like motif

53

19

400

362

0

0

94

21

100

1

60

c.91

PEP carboxykinase-like

4

2

449

0

80

0

50

100

50

1

61

c.95

Thiolase-like

13

2

4

0

4

0

46

100

46

1


DISPERSED FOLDS

62

c.47

Thioredoxin fold

51

13

1

1

1

0

45

82

82

2

63

c.12

Ribosomal proteins L15p and L18e

2

1

1

3

1

0

50

50

50

2

64

c.31

DHS-like NAD/FAD-binding domain

10

5

4

3

4

3

70

70

70

2

65

c.1

TIM beta/alpha-barrel

182

70

3

1148

1148

3

53

43

62

6

66

c.15

BRCT domain

7

4

130

12

4

2

71

86

86

2

67

c.13

SpoIIaa-like

3

2

10

4

7

3

67

67

67

2

68

c.30

PreATP-grasp domain

11

5

4

6

7

3

64

36

45

3

69

c.51

Anticodon-binding domain-like

13

6

6

35

7

0

54

69

77

2

70

c.3

FAD/NAD(P)-binding domain

46

5

7

1015

1014

7

41

41

41

8

71

c.84

Phosphoglucomutase, first 3 domains

6

1

10

94

266

10

67

67

67

2

72

c.4

Nucleotide-binding domain

7

3

46

18

14

14

57

29

29

3

73

c.9

Barstar-like

2

2

18

413

593

17

50

50

50

2

74

c.19

FabD/lysophospholipase-like

3

2

1056

940

40

40

67

67

67

2

75

c.53

Resolvase-like

9

3

444

44

65

16

44

44

44

3

76

c.97

Cytidine deaminase-like

4

2

45

411

139

28

75

75

75

2

77

c.44

Phosphotyrosine protein phosphatases I-like

3

2

52

57

120

46

67

67

67

2

78

c.58

Aminoacid dehydrogenase-like, N-terminal domain

11

5

72

404

59

32

55

55

55

3

79

c.49

Pyruvate kinase C-terminal domain-like

6

2

237

94

182

61

67

67

67

2

80

c.52

Restriction endonuclease-like

23

21

1036

216

141

128

91

57

91

3

81

c.72

Ribokinase-like

15

7

185

372

165

151

67

67

67

2

82

c.80

SIS domain

6

3

198

420

1054

23

67

67

67

2

83

c.92

Chelatase-like

11

5

311

932

221

200

36

36

36

3

84

c.60

Phosphoglycerate mutase-like

7

4

446

415

280

237

57

57

57

2

85

c.26

Adenine nucleotide alpha hydrolase-like

42

11

1017

913

460

459

29

29

29

7

86

c.94

Periplasmic binding protein-like II

25

2

654

970

592

511

96

84

88

2

87

c.66

S-adenosyl-L-methionine-dependent methyltransferases

35

23

620

908

1025

602

23

80

83

3

88

c.78

ATC-like

12

2

643

931

1048

625

42

33

58

3

89

c.35

Phosphosugar isomerase

3

2

652

940

1057

634

67

67

67

2

90

c.37

P-loop containing nucleotide triphosphate hydrolases

122

20

937

821

938

814

25

40

28

9

91

c.23

Flavodoxin-like

65

31

1045

878

1046

873

14

18

18

18

92

c.56

Phosphorylase/hydrolase-like

24

11

1035

919

1036

912

75

83

75

4

93

c.2

NAD(P)-binding Rossmann-fold domains

99

10

960

928

961

921

24

32

32

9

94

c.69

alpha/beta-Hydrolases

51

26

1059

1064

1060

1059

35

96

35

2


Ward Hierarchical Cluster Tree generated using Nres metric for VAST, SHEBA and DALI.

*Ndom, the number of domains in the fold.

#Nfam, the number of families in the fold.

§Excess Span Size is Span less Ndom; Span is the number of domains contained in the smallest cluster containing all domains of the fold.

◊ INT is the size of the intersection of the excess spans for VAST, SHEBA and DALI.

+Largest Homog. Cluster is the ratio of the size of the largest homogeneous cluster of the fold to the size of the fold itself, expressed as percent.

$Nc is the minimum number of homogeneous clusters in the fold, across VAST, SHEBA and DALI.

Table is sorted in ascending order of minimum excess span size, then in the ascending order of INT, and then by the average Largest Homog. Cluster Size value for the three methods in the descending order.

Sam et al. BMC Bioinformatics 2008 9:74   doi:10.1186/1471-2105-9-74

Open Data